scope of the gene ontology vocabularies. compile structured vocabularies describing aspects of...
TRANSCRIPT
Scope of the Gene
Ontology Vocabularies
• Compile structured vocabularies describing aspects of molecular biology
• Describe gene products using vocabulary terms (annotation)
• Develop tools:• to query and modify the vocabularies and annotations• annotation tools for curators
GO Project Goals:
DAG Structure
Directed acyclic graph: each child may have one or more
parents
Every path from a node back to the root must be biologically accurate
The True Path Rule
• is-asubclass; a is a type of b
• part-ofphysical part of (component)subprocess of (process)
Relationship Types
•Molecular Function — elemental activity or task
nuclease, DNA binding, transcription factor
•Biological Process — broad objective or
goalmitosis, signal transduction, metabolism
•Cellular Component — location or complexnucleus, ribosome, origin recognition complex
The Three Ontologies
•Molecular Function — elemental activity or task
nuclease, DNA binding, transcription factor
•Biological Process — broad objective or
goalmitosis, signal transduction, metabolism
•Cellular Component — location or complexnucleus, ribosome, origin recognition complex
The Three Ontologies
• Not a way to unify biological databases
• Not a dictated standard
• Does not define evolutionary relationships
• Additional ontologies needed to model biology and experimentation
What GO is NOT:
• Names of gene products
• Protein domains
• Protein sequence features
• Phenotypes; diseases
• Anatomical terms (except as part of terms generated by cross-products)
Terms outside the Scope of GO
• Global Open Biology Ontologies
• Umbrella site for shared genomics and proteomics vocabularies
• Present incarnation: subdirectory within GO repository:
ftp://ftp.geneontology.org/pub/go/gobo/README
The GOBO Proposal
• Open source
• Can be instantiated in DAML+OIL or GO syntax
• Orthogonal
• Shared ID space
• Defined terms
GOBO Criteria
hexose glucose fructose
DAG Cross-Products
metabolism biosynthesis catabolism
hexose metabolism hexose biosynthesis glucose biosynthesis fructose biosynthesis hexose catabolism glucose catabolism fructose catabolism glucose metabolism
... etc.
gene gene_attribute gene_structure SO gene_variation ME gene_product gene_product_attribute molecular_function GO protein_family INTERPRO phenotype mutant phenotype
anatomy
For complete current draft see ftp://ftp.geneontology.org/pub/go/gobo/README
Some GOBO Ontologies
• FlyBase & Berkeley Drosophila Genome Project • WormBase• Saccharomyces Genome Database • DictyBase• Mouse Genome Informatics • Compugen, Inc• The Arabidopsis Information Resource• Swiss-Prot/TrEMBL/InterPro
• Pathogen Sequencing Unit (Sanger Institute)
• PomBase (Sanger Institute)
• Rat Genome Database
• Genome Knowledge Base (CSHL)
• The Institute for Genomic Research
www.geneontology.org
The Gene Ontology Consortium is supported by NHGRI grant HG02273 (R01). The Gene Ontology project thanks AstraZeneca for financial support. The Stanford group acknowledges a gift from Incyte Genomics.